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annotate macros.xml @ 13:96f11a194da9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
author iuc
date Mon, 14 Jan 2019 16:48:34 -0500
parents 33a5a81e10ee
children a44cdb52201c
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1 <?xml version="1.0"?>
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2 <macros>
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96f11a194da9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
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3 <token name="@WRAPPER_VERSION@">1.3.0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement>
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7 </requirements>
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8 </xml>
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9 <xml name="version_command">
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iuc
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10 <version_command><![CDATA[
69e7d02d21fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
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11 export LC_ALL=C && kraken --version
69e7d02d21fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
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12 ]]></version_command>
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13 </xml>
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14 <xml name="input_database">
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15 <param label="Select a Kraken database" name="kraken_database" type="select">
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16 <options from_data_table="kraken_databases">
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17 <validator message="No Kraken database is available" type="no_options" />
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18 </options>
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19 </param>
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20 </xml>
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21 <xml name="citations">
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22 <citations>
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23 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
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24 </citations>
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25 </xml>
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96f11a194da9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
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26 <!-- See the kraken_databases.loc.sample documentation,
96f11a194da9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
iuc
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27 this if statement is for backward compatibility as early
96f11a194da9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
iuc
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28 versions of the wrapper assumed the UI facing field name
96f11a194da9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
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29 was also part of the directory path -->
96f11a194da9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
iuc
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30 <token name="@SET_DATABASE_PATH@">if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi</token>
96f11a194da9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
iuc
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31 <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token>
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32 </macros>